[phenixbb] Modeling Disordered Domains

van den Bedem, Henry vdbedem at slac.stanford.edu
Tue Apr 5 11:40:14 PDT 2011


That's pretty much what qFit does--it automatically adds alternate conformations (main-chain and side-chain) at occupancies it computes from a constrained fit to the data. It then uses phenix to further refine coords/adp's/occupancies. Like Nat said--you need better than 2A data.


-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Damian Ekiert
Sent: Tuesday, April 05, 2011 11:00 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Modeling Disordered Domains


Thanks for your comments.  I guess I was thinking of cases where there  
was at least some weak density, such that by setting  
"build_alternates_ringer=True", Phenix would automatically add  
alternative rotamers and refine the relative occupancies.

Regarding my disordered domains, I'm looking forward to hearing from  
Pavel about this new feature!



On Apr 4, 2011, at 11:48 AM, Nathaniel Echols wrote:

> On Mon, Apr 4, 2011 at 11:11 AM, Damian Ekiert  
> <dcekiert at scripps.edu> wrote:
>> On a final note, regarding those pesky missing side chains: any  
>> thoughts on
>> trying to employ a "Ringer"-like approach to model some of these  
>> (Fraser, et
>> al., Nature 2009, 462(7273):669-673)?  Is this practical (maybe  
>> this would
>> add to many additional parameters)?
> This is potentially useful for finding and building alternate
> conformers (something that most programs don't do - the only one I'm
> aware of is qFit: http://smb.slac.stanford.edu/qFitServer/qFit.jsp).
> But Ringer still relies on having some interpretable (albeit weak)
> density for the sidechains, and was designed to look at static rather
> than dynamic disorder.  (A somewhat artificial distinction, but
> appropriate enough when talking about refinement.)  It is also limited
> to relatively high resolution, usually better than 2.0A, not because
> of data-to-parameter ratio, but because the maps at lower resolutions
> just don't have enough detail to detect alternate conformations with
> any degree of confidence.
> Regarding missing or patchy domains, Pavel recently added a feature
> that should at least improve the phases and refinement behavior, but
> I'll let him describe it since I don't really understand what it does.
> I do not know of cases where people have found a reasonable way to
> model these explicitly, other than placing a rigid domain and letting
> the B-factors go crazy.
> -Nat
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